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“Cryptic” group-I introns in the nuclear SSU-rRNA gene of Verticillium dahliae

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Abstract

Group-I introns are widespread—though irregularly distributed—in eukaryotic organisms, and they have been extensively used for discrimination and phylogenetic analyses. Within the Verticillium genus, which comprises important phytopathogenic fungi, a group-I intron was previously identified in the SSU-rRNA (18S) gene of only V. longisporum. In this work, we aimed at elucidating the SSU-located intron distribution in V. dahliae and other Verticillium species, and the assessment of heterogeneity regarding intron content among rDNA repeats of fungal strains. Using conserved PCR primers for the amplification of the SSU gene, a structurally similar novel intron (sub-group IC1) was detected in only a few V. dahliae isolates. However, when intron-specific primers were used for the screening of a diverse collection of Verticillium isolates that originally failed to produce intron-containing SSU amplicons, most were found to contain one or both intron types, at variable rDNA repeat numbers. This marked heterogeneity was confirmed with qRT-PCR by testing rDNA copy numbers (varying from 39 to 70 copies per haploid genome) and intron copy ratios in selected isolates. Our results demonstrate that (a) IC1 group-I introns are not specific to V. longisporum within the Verticillium genus, (b) V. dahliae isolates of vegetative compatibility groups (VCGs) 4A and 6, which bear the novel intron at most of their rDNA repeats, are closely related, and (c) there is considerable intra-genomic heterogeneity for the presence or absence of introns among the ribosomal repeats. These findings underline that distributions of introns in the highly heterogeneous repetitive rDNA complex should always be verified with sensitive methods to avoid misleading conclusions for the phylogeny of fungi and other organisms.

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Acknowledgments

We are grateful to all individuals mentioned in the footnote of Table 1 for providing fungal isolates used in this study. Ioannis A. Papaioannou and this research have been co-financed by the European Union (European Social Fund—ESF) and Greek national funds through the Operational Program “Education and Lifelong Learning” of the National Strategic Reference Framework (NSRF)—Research Funding Program: Heracleitus II. Investing in knowledge society through the European Social Fund.

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  1. Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece

    Ioannis A. Papaioannou, Chrysoula D. Dimopoulou & Milton A. Typas

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  1. Ioannis A. Papaioannou
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  2. Chrysoula D. Dimopoulou
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  3. Milton A. Typas
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Correspondence to Milton A. Typas.

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Communicated by S. Hohmann.

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Papaioannou, I.A., Dimopoulou, C.D. & Typas, M.A. “Cryptic” group-I introns in the nuclear SSU-rRNA gene of Verticillium dahliae . Curr Genet 60, 135–148 (2014). https://doi.org/10.1007/s00294-013-0417-7

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